The Doctor's Wife
by Rebeccab012
Summary: Re-uploaded. The Doctor missed her. Amy didn't know she exsisted. What will he do when the memories become to much to handle, and everything spills out. How will Amy and Rory cope, when they finally find out the long awaited story, of the Doctor's past.
1. The Revalation

The Doctor's wife.

He was lonley, ever so lonley. Of course, he never let Amy or Rory know this. He enjoyed having them there, and travelling with them, but it was not the same. He had a soft spot for Amy, a special place in his heart where he held his feelings for all his companions, but it was not enough for him. Travelling around by himself for all those years had saddened him, and he missed her terribly. But, he knew there was nothing he could do to bring her back. She was gone.

Amy came bounding down the stairs – her red hair pulled back into a loose ponytail. As usual, she was wearing very little, a striped black and white t-shirt with a short black skirt and converse trainers. She smiled at the Doctor, a heartfelt smile. 'Rory's still asleep. What's wrong?' she asked, walking over to the Doctor, placing her hand on his shoulder. She knew something was wrong, for he did not return her smile as he usually did. He smiled falsely, switching switches and turning dials on the TARDIS console, pretending he was busy. 'Where do you want to go today?' He asked, changing the subject completely, avoiding her question. 'Wherever you want,' she replied softly. If there was one thing she knew, it was not to question the Doctor if he did not want to reply. If he was going to tell her, he would tell her in his own time.

He turned to Amy, and looked at her. A soft smile appeared on his face. She reminded him so much of her. She looked like her, and had many of the same characteristics as her. He couldn't bare it.

'We'll just stay here,' he said, turning around and walking down the steps to under the console. He just wanted to be alone. Amy was confused, she followed the Doctor, looking over the bannister. He was sat down on the floor, his chin resting on his knees, hugging them with both his arms. Amy was worried, she had never seen him like this before. What had he to be so upset about all of a sudden? It was only yesterday that they had been with River Song, on their way back from America. They had come back to England now, so that Amy and Rory could visit their parents after the events of the wedding. Should she leave him alone, should she help him?

Rory slipped his arm around Amy's waist. She was so preoccupied watching the Doctor that she had not noticed him approach her. He was wearing a blue shirt and jeans with black shoes. He looked remarkably smart, which pleased Amy. 'What's going on with him?' Rory asked. Amy sighed, shaking her head. 'I don't know, he has been sat there for over half an hour. He won't tell me what's wrong. He doesn't even want to go anywhere.' Rory immediately knew there was something wrong then. The Doctor always wanted to go travelling, usually ending up somewhere he shouldn't. This just wasn't like him. The Doctor buried his head in his knees. He wanted to block out everything, block out the memories from long ago which made him so sad. He was fighting against his own mind for sanity.

Amy unhooked herself from Rory's grip. She'd had enough. This wasn't like him, and she was going to find out what was wrong. She began to walk down the stairs. Rory called after her – 'Amy! Don't...' but she didn't listen. She walked over to the Doctor, and crouched in front of him. She placed her hand on his knee comfortingly. He lifted his head, part of his dark brown hair fell over his eyes. She moved it aside, and wiped a tear away that was rolling down his cheek. He had been silently crying without anyone knowing. 'Doctor, what's wrong?' She said, he voice not much louder than a whisper. Rory came down the stairs and kneeled next to Amy. He looked at the Doctor sympathetically.

The Doctor looked at them both. 'Today, the date. It's just, very sad for me,' he explained. Amy looked at him slightly confused, beckoning him to tell more with her eyes. 'Today is... today is the day that my wife died', he whispered. Another tear rolled down his face. Amy and Rory looked at each other in puzzlement. His wife?


	2. Lessons in Love

'You never said you had a wife,' Amy said. She had moved away from the Doctor, turning her back and folding her arms. Rory had sat next to the Doctor now. He understood his pain, of loving someone so much and then loosing them - he would never forget the years he waited for Amy. She was disheartened. She loved the Doctor, and loved being the only women in his life. To think that he loved another more than her, she was jealous. An awkward silence appeared. Rory turned to the Doctor.

'What happened to her?' he asked gently.

'She died. Tragic really, she was so young, so beautiful,' the Doctor replied. He smiled as he remembered her. Rory listened intently to the Doctor as he described his departed wife.

xxxxxxxxxxxx

_'You've dropped your book'. Stood in the school corridor, the Doctor was startled. Girls never spoke to him in the corridor. They normally just avoided him._

_The Doctor looked back to see a girl standing behind him. She had long red hair, it was lightly curled and bounced just above her shoulders. She had pale white skin complemented with her emerald green eyes. Her skin was darted with small brown freckles, and she had a small cupid's bow mouth, glazed in a light pink lip gloss. He stood gormless, staring at her__._

_'Your books on the floor,' she repeated. The Doctor just looked at her face. He was mesmerised by her beauty. It was her. The most popular girl in school.  
>'I..' The Doctor started to speak, but simply couldn't string enough words together. <em>

_She looked at him, slightly bewildered and bent down, picking his book up from the floor. She handed it to him and turned, walking away. The Doctor felt awkward, what did he say to a beautiful girl like that? She was tall, classy and intelligent. He was skinny and geekish. 'Thank you!' He suddenly shouted involuntarily. He covered his mouth in shock with his free hand. He was embarrassed._

_'You're welcome!' She shouted back,before turning the corner and was out of sight. He watched her go until he could no longer see her. He could not believe his luck. The prettiest girl in the whole school had just spoken to him. The Doctor turned to walk down the corridor, carrying all of his possessions this time, when he noticed something on the floor in front of him._

_On the floor was a small white flower. A lilly. Wrapped around the flower, was a pink ribbon. Attached to the thin ribbon was a note. It read:_

**_'Whenever you need a friend, come and find me. Lilly x'_**

xxxxxxxxxxxxxxxxxxxxxxxxxxx

'After that, we became really good friends' The Doctor said. 'She would quite often leave me flowers with notes on, hiding them in places she knew I'd go to. It was as if she was always one step ahead of me'. He laughed, wiping another tear from his face.

'So, you dropped your book in the corridor, and then suddenly gained a girl friend?' Amy asked, jealously raging in her voice. Rory shot an angry glance at her, as if to say 'leave him alone', but she ignored it.

'That's just how it started.' The Doctor explained. From that day in the corridor, Lilly and the Doctor began talking more often. She was no longer the popular, out of reach girl the Doctor had thought. In fact, she had liked him for a while before hand, but had been to shy to go and tell him how she felt. They began spending more and more time together, both in school and out. They would travel across Gallifrey together, going on adventures and creating memories. They would stay out under the many moons and sleep under a tree, cuddled under a shared blanket. They would go to the sea, and play in the water - acting like small children together.

She taught him how to be strong, and confident. You probably wouldn't believe it, if you saw him normally - bouncing around the TARDIS, full of life, but he was once and very timid and shy young timelord.  
>He taught her about space and time travel, talking about the stars and planets she had only ever dreamed about. They were too young to fly their own TARDIS', but they dreamed of flying one together one day.<p>

'She sounds wonderful Doctor,' Rory said, rubbing the Doctor's shoulder comfortingly.

'Yeh, totally wonderful' Amy replied sarcastically.


	3. Joined in Holy Matrimony

**THANK YOU TO EVERYONE WHO HAS REVIEWED THIS SO POSITIVLEY. Please, keep doing so, and let me know what you think.**

The Doctor stood up, and began pacing up and down the room. There wasn't much space, and he swore under his breath as he hit his head on what was the underneath of the TARDIS console. Rubbing it, he began to speak again.

'We dated for about ten years before I finally asked her to marry me. For humans, I suppose that is a long time, but on Gallifrey that was relatively short'. 'Planning the wedding, now that was the hard part. She was very precise on what she wanted - white dress, pink flowers. I wanted to wear a bow tie - bow tie's are cool, but she said no.'

'xxxxxxxxxxxx'

_The wedding was perfect. It was a beautiful sunny day, birds were singing softly in the trees. The Church was packed, full of people dressed in bright colours, all smiling and talking happily to each other. It seemed everyone on the planet had turned out to see the wedding of the most perfect couple. Important time Lords and Ladies sat on thrones on one side of the aisle, dressed in their traditional red and gold attire. The Doctor nodded to them as he stood waiting. A huge stained glass window allowed light to burst through into the church. Planets, stars and tardis's were stained into the window, showing the history of the home planet. A long the sides of the aisle were delicate white ribbons, decorated with tiny small pink roses. It was truly beautiful. _

_The Doctor was nervous. His hands were shaking, and he could feel his hearts pumping rapidly in his chest. Adrenaline raced around his body. A friendly hand appeared on his shoulder. He turned to see the Master looking reassuringly at him. This was a time when the two were still friends. The Doctor had picked him to be his best man, his oldest and most dearest friend.. for the moment. 'You'll be fine Doctor, I promise. Just wait until you see how she looks'. A best man was not a Gallifreyan tradition, and the Master was slightly uncertain of what the job entailed. The Doctor explained that he had seen it on Earth, and he had liked it. He then tried to explain to the Master what a 'stag do' was, and they drew the line there. After all, the Doctor DID NOT like wine._

_Two more minutes._

_The Gallifreyan wedding march rang through the church, and everyone stood. The traditionally carved wooden doors at the back of the church opened, and Lilly walked in. She had a white veil covering her face, and her long red hair was pinned up on the back of her head. She wore a white dress with a fitted rouched body. The sweetheart neckline was accented by an original hand-beaded and embroided design. A white, rose arrangement gathered the skirt at the back, drawing attention to the long, elegant train. She held a delicate bouquet of matching pink flowers to the decorations in the church in front of her._

_The Doctor couldn't stop smiling. He couldn't believe how beautiful she looked. She smiled too. But, there was something hidden behind her smile. Something which the Doctor was oblivious too._

_The Priest began the ceremony. Traditional Gallifreyan hymns were sung, readings were read and prayers were said. The Priest spoke to the couple, blessing them with Holy Gallifreyan water. _

_'It's time for the bride's personal vow,' The Priest said._

_Lilly nodded, taking the Doctor's hands in hers._

_'I have never met anyone quite like you before. You are the light in my life, and without it... I simply do not know what I would do without you. From first meeting you, I knew that I would that we would spend the rest of our lives together. You're intelligent, handsome and extremley skinny..' - everyone laughed, including the Doctor. It was not something he hadn't heard before. 'and you are everything that I look for in a man. I want to spend the rest of my life with you. I want to travel through time and space, holding your hand every step of the way. Because, I know that you'll need somebody to make sure you behave yourself. I love you, with all of my soul.'_

_The Doctor smiled, mouthing a small 'thank you' of appreciation to Lilly._

_The ceremony was coming to a close. The Doctor had said his personal vow, attempting to merge humour with his expressions of love. 'Bow ties are cool' was frequently mentioned, much to the annoyance of Lilly._

_The Priest, praying to the Gods, expressed to the couple that they could finally kiss._

_'I love you,' said the Doctor._

_'I love you too' Lilly replied._

_And they kissed._

'xxxxxxxxxxxxx'

'That was supposed to be the best day of our lives', The Doctor said. Amy, feeling slightly sympathetic towards the Doctor now, had sat next to Rory, leaning her head against his shoulder. Perhaps, her feelings about her own wedding, and her love for Rory, made her realise just how sorry she felt for the Doctor.

'But, I'm guessing it wasn't?' Rory asked tentatively.

'Oh no'. The Doctor said. 'This was just the start of something. Something terrible'.


	4. A new arrival?

The Doctor turned away from them. He had said too much. He sighed, fiddling with his bow tie. Amy looked at Rory. He shrugged his shoulders gently, he did not know what to say.

Amy looked at the Doctor. She was worried now, more than she had ever been for him She did not know what to do, or what to say. This was the first time she had ever seen the Doctor express such emotions, and it frightened her slightly to see him so on edge.

The Doctor knew he must finish the story. He could not leave them simply wondering, even when it was agonising to tell.

'It was just two months after that day it really all went wrong,' he said, still with his back to them. Amy moved back to Rory and they listened intently, sympathising with the broken hearted man.

'She tried to tell me, and I wouldn't listen.'

xxxxxxxxxxxxxxxxxxxxxxxxxxxxx

_'Positive'. She looked down at the white stick, and her hearts skipped a beat. _

_No._

_Not now. _

_She was shocked. Her chest was tight, and she couldn't breathe. This could not have happened at a worse time. She began to cry, silently so that he wouldn't hear. Not that he would care if she was, he was pre-occupied. _

_A large bang exploded outside the house, and the whole room shook. Another house had been attacked. The time war was once again, under way, for the seventh day. She stedied herself against the wall until the quake stopped, and sat down on the edge of the toilet seat. _

_She had to tell him, she had no choice. He deserved to know. But, how could they raise a baby in this war driven society? He barely paid her the time of day, he was too busy fighting. How could they raise a baby?_

_She took a deep breath, and stood. She turned the handle on the bathroom door, and went to find him. She turned left into the living room. The room was bare, only a few chairs and table. He was sat in the chair, staring at the wall opposite him. It was unusual to find him indoors when the fighting was going on, he never left the battlefield. He was distant now, the war had left him cold, and uninterested. She moved slowly towards him, clutching the white stick in her hand._

_He looked up at her, his eyes slowly softening as he realised who she was._

_'Hey,' she said comfortingly, with a gentle smile._

_'Three more dead,' he said. His voice no louder than a whisper. His eyes filled with tears, which he fought back. He never carried a weapon, until now. He never fought, until now. He hated loosing people._

_'I came inside.. I can't do this any more..' he cried. _

_'Hey.. shh. Come on, it's ok. You are trying you best to save them', she replied._

_She moved towards him again, and stood in front of him. He didn't look up at her again, but stared back at the wall once more. She knew there was never going to be a right time to tell him, but she had to do it now, before he left again._

_'Sweetheart, I have some news..' she began._

_Another explosion. Another quake._

_Startled, broken from his trance, he looked out of the window. Yellow fire soared into the air, the flames dancing in the breeze. He got up quickly and moved towards the door._

_She followed, trying to stop him._

_'No please, Doctor, stay.. I need to tell you..'_

_'I have to go' he stated, opening the door._

_'No! Doctor, I'm...'_

_And he was gone._

_'...pregnant'._

_xxxxxxxxxxxxxxxxxxxxxxxxxxxx_

_'I found out when it was to late.' The doctor sighed._


	5. The Capture

'Oh Doctor,' Amy replied. A tear slid down her face. She was no longer jealous of this woman, she felt so sorry for her. Rory hugged her tightly, also feeling overwhelmed by emotion. He couldn't bare the thought of loosing Amy, especially carrying their child.

The Doctor turned and faced them again. His face was red and swollen from the tears. 'It was too late by then. They'd taken her by the time I got back.'

'Taken her? Who took her?' Rory asked.

'The Daleks', he replied. 'They knew taking her would get to me. I tried to find her, I searched and searched. Nothing.'

'That's why you started travelling? To find her?' Amy said, already knowing the answer to her own question.

The Doctor nodded. 'Having a companion, a female.. I thought it would ease the pain. It didn't.' And you Pond...' He walked over to Amy, and looked her in the eyes. 'You look so much like her.' A small smile appeared on his face as he remembered Lilly.

Yet, he knew nothing of the pain she suffered for him.

xxxx

_The pain was agonising._

_For days, she had been away from him. Captured, alone and afraid._

_Chained by her hands to the a long metal pole, her body was limp and lifeless. She could barely breathe. Another laser flew across the room, and hit her in the chest. She let out another blood curdling scream, as her body writhed, contorting through the pain. A tear rolled down her cheek, as she slowly raised her head to look at them. _

_Around her wrist, was a square metal device. Dalek technology. They made her wear it. The device used stopped Lilly from regenerating, almost making her human._

_'Tell us. Where is the Doctor?' they chorused. One moved closer to her, staring at her through it's eye. _

_Her hair was hanging over her eyes. 'I will never tell'._

_'Tell us. Tell us,' they repeated._

_'You've killed my baby, my family, and destroyed my home. Do you think I'd let you take the last precious thing in my life? The most important man in the universe,' Lilly laughed weakly. 'Never'._

_Another laser pierced her through the chest, and her hearts finally surrendered to the pain._

_'Good bye my Doctor. I love you'. _

_xxxxxxxxxxxxxxxx_


	6. The Last Entry

_**NOTE: These song lyrics are not owned by me, but by the lyricist of the musical Ragtime. **_

It had been a few hours since the revelation of Lilly's death. Amy, Rory and The Doctor had come back up from under the console. The TARDIS had landed in a small town on the outskirts of Cardiff, parked at the end of an alleyway. Amy was sat on the doorstep of the TARDIS, the doors open behind her. Rory walked towards her, carrying two cups of coffee from the coffee shop on the other side of the road. He handed her one, and sat down next to her. She thanked him, leaning her head on his shoulder.

'I never thought something so sad could happen to him,' Amy said, as she sipped her coffee. 'He's such a brave, strong man...'

'I know, but it makes you wonder, if she hadn't of died, we would never have met him,' Rory replied.

The two continued to talk.

Inside the TARDIS, the Doctor was in a room down one end of the east corridor, just past the swimming pool. The room was painted cream, with a bed along one of the walls. This was Amy and Rory's room. Along the otherwall, was a wardrobe. He opened it, pushing Amy and Rory's clothes to one side. At the back of the wardrobe, was a small pink box. He took it from the wardrobe, and sat down on the wouldn't mind, it would only be for a minute. He knew that box was there, he had always known. He just never had the strenghth to open it.

He lifted the lid of the box, revealing a small notebook inside, alongside two rings and a broach. He lifted the notebook out gently, and opened it, placing the box on his lap. Upon opening it,he revealed a note on the first page. It was written in small delicate handwriting. Handwriting that he recognised straight away.

_'In this box, I keep my most treasured possessions. Firstly, my wedding and engagement rings, from the man I love. Keep those safe, treasure them as much as I did. Secondly, a broach given to me by my Grandmother, said to contain the most valuable memories of the wearer, if anything should happen to them. Wear it, remember me always. Lastly, this notebook, containing everything I have ever thought about. My dreams, my hopes. Read it. Read it and understand everything. You need to. My love always, Lilly.'_

As always, she knew he would read it. Always one step ahead of the Doctor. He smiled, and began reading through the pages. The day they met, their first date, their wedding... it was all there.

The last entry, however, was different to the others. The handwriting was eratic and untidy, as if it was written in a rush. It was unlike anything he had read before in the book. It was dated from just days before she died.

_'there was a time_  
><em>our happiness seemed neverending.<em>  
><em>i was so sure<em>  
><em>that where we were heading was right.<em>  
><em>life was a road<em>  
><em>so certain and straight and unbending.<em>  
><em>our little road<em>  
><em>with never a crossroad in sight.<em>

_there was a time_  
><em>when you were the person in motion.<em>  
><em>i was your wife.<em>  
><em>it never occurred to want more.<em>  
><em>you were my sky,<em>  
><em>my moon and my stars and my ocean.<em>  
><em>we can never go back to before.'<em>

He realised then, just how unhappy she had been. They could never go back to how it was before. Before the war. She was gone, and it was all his fault.

Another companion lost. The love of his life, lost.


End file.
